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NM_001353345.2(SETD1B):c.5704C>T (p.Arg1902Cys) AND Inborn genetic diseases

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 30, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001267570.5

Allele description [Variation Report for NM_001353345.2(SETD1B):c.5704C>T (p.Arg1902Cys)]

NM_001353345.2(SETD1B):c.5704C>T (p.Arg1902Cys)

Gene:
SETD1B:SET domain containing 1B, histone lysine methyltransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q24.31
Genomic location:
Preferred name:
NM_001353345.2(SETD1B):c.5704C>T (p.Arg1902Cys)
Other names:
R1859C; NM_015048.1:c.5575C>T
HGVS:
  • NC_000012.12:g.121828047C>T
  • NM_001353345.2:c.5704C>TMANE SELECT
  • NP_001340274.1:p.Arg1902Cys
  • NC_000012.11:g.122265953C>T
  • NM_001353345.1:c.5704C>T
Protein change:
R1902C; ARG1859CYS
Links:
OMIM: 611055.0002; dbSNP: rs1876922399
NCBI 1000 Genomes Browser:
rs1876922399
Molecular consequence:
  • NM_001353345.2:c.5704C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001445752Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Jun 30, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

De novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.

Hiraide T, Nakashima M, Yamoto K, Fukuda T, Kato M, Ikeda H, Sugie Y, Aoto K, Kaname T, Nakabayashi K, Ogata T, Matsumoto N, Saitsu H.

Hum Genet. 2018 Jan;137(1):95-104. doi: 10.1007/s00439-017-1863-y. Epub 2018 Jan 10.

PubMed [citation]
PMID:
29322246

Details of each submission

From Ambry Genetics, SCV001445752.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.5575C>T (p.R1859C) alteration is located in coding exon 16 of the SETD1B gene. This alteration results from a C to T substitution at nucleotide position 5575, causing the arginine (R) at amino acid position 1859 to be replaced by a cysteine (C). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been determined to be the result of a de novo mutation in two individuals with features consistent with SETD1B-related neurodevelopmental disorder (Hiraide, 2018; Ambry internal data). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024